This is a shiny app for chromosomal copy number variant analysis. It can parse the vcf file with SV calls, visualize CNV and B-allele frequency and genetic phasing information interactively.
R version >= 3.6.3 Following R libraries are required:
Shifting level models based segmentation is performed using SLMSuite.
Launch app on local with the main branch:
shiny::runGitHub(repo = "BCM-Lupskilab/VizCNV")
or Launch app on local with the dev branch:
shiny::runGitHub(repo = "cluhaowie/VizCNV",ref="dev")
A docker image is public available through docker hub docker pull duclare123/vizcnv_dev
Upload the required file from local file systerm:
If launch the app on cloud or on server, input file need to be upload due to access restriction.
Visualize the CNV calls in table format, read depth plot and B-allele
frequency together:
The app require read depth file as the input: A output from mosedepth can be used example of generate the read depth file for 1Kb window size would be:
mosdepth -n --fast-mode --by 1000 sample.wgs $sample.wgs.cram